MolNFT v1 · #111358 · protein
HKU4 3CLPRO bound to non-covalent inhibitor 2A
4YOJ · 3C-like proteinase: “HKU4 3CLPRO bound to non-covalent inhibitor 2A”. X-ray diffraction, 1 ligand (RFM), 8 pockets (best druggability 0.77). MolNFT v1 #111358 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4YOJ
- Type
- protein
- Length
- 612 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase
- EC
- 3.4.22.-
- UniProt
- P0C6W3
- Ligands
- RFM
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3C-like proteinase (EC 3.4.22.-) | protein | 306 | 25% helix, 30% strand | P0C6W3 |
Ligands and binding sites
- RFM · N-{4-[(1H-benzotriazol-1-ylacetyl)(thiophen-3-ylmethyl)amino]phenyl}benzamide · ligand · 2 copies · chains A, B
- ACT · Acetate ion · additive · 3 copies · chains A, B
- FMT · Formic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1047 | 0.77 | 0.79 | 77 | ACT |
| 2 | 431 | 0.64 | 0.77 | 54 | empty |
| 3 | 240 | 0.56 | 0.78 | 35 | RFM |
| 4 | 210 | 0.53 | 0.77 | 36 | RFM |
| 5 | 71 | 0.50 | 0.84 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1295 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 4YOJ · HKU4 3CLpro bound to non-covalent inhibitor 2A · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P0C6W3
- Elsewhere: RCSB PDB 4YOJ · PDBe 4YOJ · UniProt P0C6W3
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